Contacts of the helix formed by residues 154 - 162 (chain A) in PDB entry 3V9G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A MET* 4.2 2.0 - - - -
152A GLY 3.9 0.8 + - - +
153A LYS* 1.3 76.6 - - - +
155A VAL* 1.3 67.9 + - - +
156A ILE* 3.9 4.2 - - - +
157A GLN* 3.2 24.0 + - + +
158A ALA* 3.0 20.8 + - - +
343A TYR* 5.4 1.5 - - - +
380A PRO* 4.0 13.0 - - + -
386A THR* 3.6 22.4 - - + +
387A PHE 3.2 30.7 + - - +
388A PHE* 3.9 11.2 - - - -
389A SER 4.7 1.3 - - - +
561B TYR* 3.6 15.9 + - - -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.7 41.3 - - + -
50A LEU* 3.9 13.2 - - + -
144A LEU* 4.9 1.4 - - - +
148A MET* 3.8 21.7 - - + +
154A THR* 1.3 74.8 - - - +
156A ILE* 1.3 59.1 + - - +
158A ALA* 3.3 3.1 + - - +
159A GLU* 3.0 25.5 + - - +
380A PRO 4.7 0.8 + - - +
384A PHE* 3.7 37.5 - - + -
561B TYR* 3.4 25.0 + - + -
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.1 18.4 - - + -
38A LEU 4.5 7.0 - - - +
39A ALA 6.1 0.7 - - - +
40A PHE* 5.6 2.5 - - + -
154A THR* 3.9 6.1 - - - +
155A VAL* 1.3 77.3 - - + +
157A GLN* 1.3 77.4 + - - +
159A GLU* 4.2 8.3 - - + -
160A ILE* 3.1 39.6 + - + +
342A GLU* 4.7 0.2 - - - +
387A PHE 5.9 0.2 - - - +
559B TYR* 3.8 43.5 - - + -
561B TYR* 3.7 33.5 + - + +
562B MET* 5.8 0.2 - - - -
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LYS* 3.4 26.6 + - + +
154A THR* 3.2 20.9 + - - +
156A ILE* 1.3 84.2 - - - +
158A ALA* 1.3 65.8 + - - +
160A ILE* 3.6 21.1 - - - +
161A ASP* 3.2 25.1 + - - +
342A GLU* 3.3 33.8 + - + -
343A TYR* 4.1 21.4 - - + +
347A LYS* 2.8 33.7 + - - +
387A PHE 5.6 1.1 - - - +
559B TYR* 4.5 2.0 + - - -
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.2 28.9 - - + +
147A THR* 4.2 12.6 - - - -
148A MET* 3.7 23.1 - - + -
153A LYS* 4.1 11.2 - - + +
154A THR 3.0 16.3 + - - +
155A VAL 3.7 4.3 - - - +
157A GLN* 1.3 77.8 - - - +
159A GLU* 1.3 58.1 + - - +
162A ALA* 2.8 27.3 + - - +
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.4 23.2 - - + -
38A LEU* 2.7 25.0 + - - +
40A PHE* 3.6 29.7 - - + -
140A ARG* 2.6 35.1 + - - -
144A LEU* 3.7 17.2 - - + +
155A VAL 3.0 18.0 + - - +
156A ILE* 3.7 11.7 - - + +
157A GLN 3.2 0.2 - - - -
158A ALA* 1.3 78.9 - - - +
160A ILE* 1.3 58.8 + - - +
161A ASP 3.4 0.2 + - - -
163A ALA* 3.4 6.6 - - - +
164A ALA* 3.0 25.5 + - - +
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Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.3 14.8 - - + -
156A ILE* 3.1 30.9 + - + +
157A GLN* 3.6 39.5 - - - +
159A GLU* 1.3 76.8 - - - +
161A ASP* 1.3 61.6 + - + +
164A ALA* 3.8 9.4 - - + +
165A GLU* 3.2 27.4 + - - +
212A PHE* 5.5 6.1 - - + -
347A LYS* 4.6 7.4 - - - +
509A LYS* 6.2 1.3 - - - +
512A GLY* 5.6 9.6 - - - -
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A THR* 4.0 0.9 - - - +
153A LYS* 3.2 29.9 - - - +
157A GLN 3.2 16.3 + - - +
158A ALA 4.0 0.7 - - - +
159A GLU 3.2 0.4 - - - -
160A ILE* 1.3 78.2 - - + +
162A ALA* 1.3 69.2 + - - +
163A ALA 3.1 2.6 + - - -
165A GLU* 3.5 8.2 + - - -
166A LEU 3.3 21.8 + - - -
212A PHE* 3.4 21.7 - - + -
213A THR* 3.1 22.7 + - - -
214A ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 4.6 3.1 - - - +
143A ILE* 3.6 33.9 - - + +
144A LEU* 4.3 1.6 - - + -
147A THR* 3.3 29.6 - - + +
158A ALA 2.8 15.7 + - - +
161A ASP* 1.3 78.7 - - - +
163A ALA* 1.3 58.7 + - - +
166A LEU* 3.6 21.6 - - - +
213A THR* 3.9 12.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il